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discounted EARLY registration ends Dec 31, 2014
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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Compound: L-ornithine

Synonyms: Ornithine, 2, 5-diaminovaleric acid, 2, 5-diaminopentanoic acid, 2, 5-diaminopentanoate, α,δ-diaminovaleric acid

Superclasses: an amino acid or its derivative an amino acid an alpha amino acid a non-standard alpha amino acid ornithine
an amino acid or its derivative an amino acid an alpha amino acid a non-standard alpha amino acid
an amino acid or its derivative an amino acid an L-amino acid

Chemical Formula: C5H13N2O2

Molecular Weight: 133.17 Daltons

Monoisotopic Molecular Weight: 132.0898776398 Daltons

SMILES: C(C[N+])CC([N+])C([O-])=O

InChI: InChI=1S/C5H12N2O2/c6-3-1-2-4(7)5(8)9/h4H,1-3,6-7H2,(H,8,9)/p+1/t4-/m0/s1

InChIKey: InChIKey=AHLPHDHHMVZTML-BYPYZUCNSA-O

Unification Links: ChEBI:46911 , ChemSpider:5360242 , HMDB:HMDB00214 , IAF1260:37976 , KEGG:C00077 , MetaboLights:MTBLC46911 , PubChem:6992088

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): 47.5525 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

arginine degradation VII (arginase 3 pathway) , ornithine degradation I (proline biosynthesis) :
L-ornithine → L-proline + ammonium

gramicidin S biosynthesis :
D-phenylalanyl-[gramicidin-S synthetase] + L-proline + L-valine + L-ornithine + L-leucine + 4 ATP → D-phenylalanyl-L-prolyl-L-valyl-L-ornithyl-L-leucyl-[NRPS-pcp] + 4 AMP + 4 diphosphate + 4 H+

L-Nδ-acetylornithine biosynthesis :
L-ornithine → L-Nδ-acetylornithine

ornithine lipid biosynthesis :
L-ornithine + a (3R)-3-hydroxyacyl-[acyl-carrier protein] → a lyso-ornithine lipid + a holo-[acyl-carrier protein] + H+

putrescine biosynthesis III , putrescine biosynthesis IV , superpathway of ornithine degradation :
L-ornithine + H+ → CO2 + putrescine

pyoverdine I biosynthesis :
L-ornithine + NADPH + oxygen → N5-hydroxy-L-ornithine + NADP+ + H2O

Not in pathways:
L-ornithine + NAD(P)H + oxygen → N5-hydroxy-L-ornithine + NAD(P)+ + H2O
L-ornithine + 2-oxoglutarate + NADPH + H+ → ornaline + NADP+ + H2O

prodigiosin biosynthesis :
(S)-3-acetyloctanal + an L-amino acid → 2-methyl-3-n-amyl-dihydropyrrole + a 2-oxo acid + H2O

rhizocticin A and B biosynthesis :
2-keto-5-phosphono-3-cis-pentenoate + an L-amino acidL-2-amino-5-phosphono-3-cis-pentenoate + a 2-oxo carboxylate
2-keto-4-hydroxy-5-phosphonopentanoate + an L-amino acid → 2-amino-4-hydroxy-5-phosphonopentanoate + a 2-oxo carboxylate


ATP + 2 an L-amino acid → ADP + a dipeptide + phosphate + H+

Reactions known to produce the compound:

arginine biosynthesis II (acetyl cycle) :
L-glutamate + N-acetyl-L-ornithine → N-acetyl-L-glutamate + L-ornithine

arginine biosynthesis IV (archaebacteria) :
an [L-2-aminoadipate carrier protein]-L-ornithine + H2O → L-ornithine + a [LysW protein]-L-glutamate

creatine biosynthesis :
glycine + L-arginine → guanidinoacetate + L-ornithine

D-cycloserine biosynthesis :
Nω-hydroxy-L-arginine + H2O → L-ornithine + hydroxyurea

proline biosynthesis II (from arginine) :
L-citrulline + 2 H+ + H2O → L-ornithine + CO2 + ammonium

streptomycin biosynthesis :
L-arginine + 1-amino-1-deoxy-scyllo-inositol 4-phosphate → 1-guanidino-1-deoxy-scyllo-inositol 4-phosphate + L-ornithine
N1-amidinostreptamine 6-phosphate + L-arginine → streptidine 6-phosphate + L-ornithine

γ-glutamyl cycle :
an (γ-L-glutamyl)-L-amino acid → an L-amino acid + 5-oxoproline

Not in pathways:
a peptide + H2O → an L-amino acid + a peptide
a peptide + H2O → a peptide + an L-amino acid
a N-methyl L-amino acid + oxygen + H2O → an L-amino acid + formaldehyde + hydrogen peroxide
a polypeptide + H2O → a polypeptide + an L-amino acid


amino acids(n) + H2O → amino acids(n-1) + an α amino acid
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a protein + H2O → a protein + an α amino acid

Reactions known to both consume and produce the compound:

arginine biosynthesis I (via L-ornithine) , arginine biosynthesis II (acetyl cycle) , arginine biosynthesis IV (archaebacteria) , citrulline degradation :
L-ornithine + carbamoyl-phosphate ↔ L-citrulline + phosphate + H+

arginine degradation I (arginase pathway) :
L-arginine + H2O ↔ urea + L-ornithine
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

arginine degradation VI (arginase 2 pathway) :
L-arginine + H2O ↔ urea + L-ornithine
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

arginine degradation VII (arginase 3 pathway) , putrescine biosynthesis IV :
L-arginine + H2O ↔ urea + L-ornithine

citrulline biosynthesis :
L-arginine + H2O ↔ urea + L-ornithine
L-ornithine + carbamoyl-phosphate ↔ L-citrulline + phosphate + H+
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

L-Nδ-acetylornithine biosynthesis :
L-arginine + H2O ↔ urea + L-ornithine
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

ornithine biosynthesis :
N-acetyl-L-ornithine + H2O ↔ L-ornithine + acetate

ornithine de novo biosynthesis , proline biosynthesis III :
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

ornithine degradation II (Stickland reaction) :
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde
L-ornithine ↔ D-ornithine

proline biosynthesis II (from arginine) :
L-ornithine + carbamoyl-phosphate ↔ L-citrulline + phosphate + H+
L-ornithine + 2-oxoglutarate ↔ L-glutamate + L-glutamate-5-semialdehyde

proline biosynthesis IV :
L-ornithine + 2-oxoglutarate ↔ L-glutamate + 2-keto-ornithine

urea cycle :
L-arginine + H2O ↔ urea + L-ornithine
L-ornithine + carbamoyl-phosphate ↔ L-citrulline + phosphate + H+

Not in pathways:
L-ornithine + a 2-oxo carboxylate ↔ a standard α amino acid + L-glutamate-5-semialdehyde
L-ornithine[chloroplast stroma] + carbamoyl-phosphate[chloroplast stroma] ↔ L-citrulline[chloroplast stroma] + phosphate[chloroplast stroma] + H+[chloroplast stroma]
L-ornithine + 2-oxoglutarate ↔ 1-pyrroline-5-carboxylate + L-glutamate + H+ + H2O


L-alanine + a 2-oxo carboxylate ↔ pyruvate + an L-amino acid

In Reactions of unknown directionality:

Not in pathways:
N5-(L-1-carboxyethyl)-L-ornithine + NADP+ + H2O = pyruvate + L-ornithine + NADPH + H+
L-arginine + L-lysine = homoarginine + L-ornithine
L-ornithine + succinyl-CoA = N2-succinyl-L-ornithine + coenzyme A + H+
L-ornithine + 2 benzoyl-CoA = N2,N5-dibenzoyl-L-ornithine + 2 coenzyme A + 2 H+


an L-amino acid = a D-amino acid
an L-amino acid + NAD+ + H2O = a 2-oxo carboxylate + ammonium + NADH + H+
an N-carbamoyl-L-amino acid + H2O + 2 H+ = an L-amino acid + ammonium + CO2
S-ureidoglycine + a 2-oxo carboxylate = oxalurate + an L-amino acid


a 5-L-glutamyl-[peptide] + an amino acid = a 5-L-glutamyl-amino acid + a peptide

In Transport reactions:
L-ornithine[cytosol]L-ornithine[mitochondrial lumen] ,
putrescine[cytosol] + L-ornithine[periplasmic space] → putrescine[periplasmic space] + L-ornithine[cytosol] ,
ATP + L-ornithine[periplasmic space] + H2O → ADP + L-ornithine[cytosol] + phosphate + H+ ,
an L-amino acid[cytosol]an L-amino acid[periplasmic space]

Enzymes activated by L-ornithine, sorted by the type of activation, are:

Activator (Allosteric) of: carbamoyl phosphate synthetase [Anderson77, Trotta74] , arginase [Colleluori01]

Enzymes inhibited by L-ornithine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: acetylornithine deacetylase [Comment 1] , arginine decarboxylase, degradative [Blethen68] , lysine:cadaverine antiporter [Soksawatmaekhin04] , cadaverine:H+ symporter [Soksawatmaekhin04] , L-arginine:glycine amidinotransferase [Sipila80] , arginine deiminase [Hill67] , arginase [Editors93] , arginase [Schrell89]

Inhibitor (Noncompetitive) of: agmatinase [Satishchandran86]

Inhibitor (Allosteric) of: arginine deiminase [Monstadt91, Comment 2]

Inhibitor (Mechanism unknown) of: S-methyl-L-methionine decarboxylase [Kocsis00] , L-lysine-α-ketoglutarate reductase [Hutzler75] , ornithine carbamoyltransferase [Comment 3]


References

Anderson77: Anderson PM (1977). "Binding of allosteric effectors to carbamyl-phosphate synthetase from Escherichia coli." Biochemistry 1977;16(4);587-93. PMID: 189806

Blethen68: Blethen SL, Boeker EA, Snell EE (1968). "Argenine decarboxylase from Escherichia coli. I. Purification and specificity for substrates and coenzyme." J Biol Chem 1968;243(8);1671-7. PMID: 4870599

Colleluori01: Colleluori DM, Morris SM, Ash DE (2001). "Expression, purification, and characterization of human type II arginase." Arch Biochem Biophys 389(1);135-43. PMID: 11370664

Editors93: Editors: Abraham L. Sonenshein, James A. Hoch, Richard Losick (1993). "Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics." American Society For Microbiology, Washington, DC 20005.

Hill67: Hill DL, Chambers P (1967). "The biosynthesis of proline by Tetrahymena pyriformis." Biochim Biophys Acta 148(2);435-47. PMID: 6075416

Hutzler75: Hutzler J, Dancis J (1975). "Lysine-ketoglutarate reductase in human tissues." Biochim Biophys Acta 377(1);42-51. PMID: 235294

Issaly74: Issaly IM, Issaly AS (1974). "Control of ornithine carbamoyltransferase activityby arginase in Bacillus subtilis." Eur J Biochem 1974;49(3);485-95. PMID: 4216455

JavidMajd00: Javid-Majd F, Blanchard JS (2000). "Mechanistic analysis of the argE-encoded N-acetylornithine deacetylase." Biochemistry 2000;39(6);1285-93. PMID: 10684608

Kocsis00: Kocsis MG, Hanson AD (2000). "Biochemical evidence for two novel enzymes in the biosynthesis of 3-dimethylsulfoniopropionate in Spartina alterniflora." Plant Physiol 123(3);1153-61. PMID: 10889264

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Monstadt91: Monstadt GM, Holldorf AW (1991). "Arginine deiminase from Halobacterium salinarium. Purification and properties." Biochem J 1991;273 ( Pt 3);739-45. PMID: 1847623

Satishchandran86: Satishchandran C, Boyle SM (1986). "Purification and properties of agmatine ureohydrolyase, a putrescine biosynthetic enzyme in Escherichia coli." J Bacteriol 1986;165(3);843-8. PMID: 3081491

Schrell89: Schrell A, Alt-Moerbe J, Lanz T, Schroeder J (1989). "Arginase of Agrobacterium Ti plasmid C58. DNA sequence, properties, and comparison with eucaryotic enzymes." Eur J Biochem 184(3);635-41. PMID: 2806247

Sipila80: Sipila I (1980). "Inhibition of arginine-glycine amidinotransferase by ornithine. A possible mechanism for the muscular and chorioretinal atrophies in gyrate atrophy of the choroid and retina with hyperornithinemia." Biochim Biophys Acta 613(1);79-84. PMID: 7378422

Soksawatmaekhin04: Soksawatmaekhin W, Kuraishi A, Sakata K, Kashiwagi K, Igarashi K (2004). "Excretion and uptake of cadaverine by CadB and its physiological functions in Escherichia coli." Mol Microbiol 51(5);1401-12. PMID: 14982633

Trotta74: Trotta PP, Pinkus LM, Haschemeyer RH, Meister A (1974). "Reversible dissociation of the monomer of glutamine-dependent carbamyl phosphate synthetase into catalytically active heavy and light subunits." J Biol Chem 1974;249(2);492-9. PMID: 4358555


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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